The Secure Service can easily be configured to use a proxy server for all of its communications.
The Secure Service will automatically be configured to use the proxy if it is installed with the Exoprise Management Client and you choose to set it up with a proxy during installation.
If you are installing the Secure Service manually (bulk-deployment) or you want to have more control over the proxy configuration for the Secure Service then you can edit the registry. Proxy PAC files are not supported in this way.
Additionally, you can remove the registry settings and the service will automatically use the proxy environment that is configured for the account that the service is running under. Proxy PAC files can be supported this way. This is most often used with service accounts as opposed to Local System accounts. When the Secure Service is run as a domain user (sometimes referred to as a service account), the proxy settings can be managed with Active Directory/GPO.
For the registry, the root key for the Secure Service proxy settings on 32-bit machines is:
On 64bit machines, the root key is:
The following keys are available for controlling the proxy for the Secure Service Shell
Once you've updated the registry, the service should be restarted for the changes to take affect.